1. Nkx-1.2 Homeobox Gene: A mouse homeobox gene, Nkx-1.2, (previously termed Sax-1) that is closely related to the Drosophila NK-1/S59 gene was cloned, and genomic DNA and cDNA were sequenced. Nine Nkx-1.2 cDNA clones were found that correspond to three species of Nkx-1.2 mRNA that are formed by alternative splicing at conventional 5' donor and 3' acceptor splice sites; however, seven cDNA clones were found that correspond to three species of Nkx-1.2 RNA from testes that have novel TG/AC 5' and 3' splice sites. The consensus splice sequences are: 5'donor, CC/TGGAAG; 3' acceptor, ACTTAC/. Predicted amino acid sequences suggest that some transcripts may be translated into proteins that lack part or all of the homeodomain. At least three bands of Nkx-1.2 mRNA were found in RNA from the testes. Nkx-1.2 mRNA was shown to be present in postmeiotic germ cells of the testis and in mature spermatozoa. Nkx-1.2 mRNA also was found in regions of the adult cerebral cortex, hippocampus, diencephalon, pons/medulla, and cerebellum. Nkx-1.2 mRNA was found in embryos in highest abundance in 10-day embryos; the mRNA levels decrease during further development. Nkx-1.2 mRNA also was found in discrete zones of the embryonic mesencephalon and myelencephalon. 2. Sebox Homeobox Gene: Sebox is a mouse paired-like homeobox gene, previously named OG-9. Sebox genomic DNA and cDNA were cloned and sequenced. In addition, rat and human Sebox genomic DNAs were cloned and sequenced, and the predicted amino acid sequences were compared. The mouse Sebox gene is expressed in brain, skin, ovary, and liver. In the brain, the Sebox gene is expressed in the cerebral cortex and CA areas of the hippocampus, pontine nuclei, choroid plexus, and the cerebellum. Northern analysis and RNase protection assays revealed low levels of Sebox RNA in 12-day mouse embryos and higher levels in 18- and 19-day embryos. In late embryos and newborn mice, Sebox expression is localized in the epidermis. In adult mice, Sebox RNA was found in maturing oocytes and in fertilized eggs; however, the abundance of Sebox RNA is decreased in the two-cell embryo, and little or none was detected in the four-cell embryo. Hence, Sebox is a maternally expressed homeobox gene.